Current Topics in Medicinal Chemistry - Volume 16, Issue 21, 2016

Botulinum neurotoxins (BoNTs), the most potent known toxins, cause severe muscle paralysis and death at nanogram exposures and are considered biothreat agents. BoNTs target the neuromuscular junction where they release smaller zinc metalloprotease light chains (LCs) into the neuron cytosol that selectively cleave SNARE proteins and thus block the exocytosis of acetylcholine neurotransmitters necessary for skeletal muscle contraction. The majority of efforts to develop post-symptomatic therapeutics for botulism poisoning have focused on inhibiting the LC and tremendous strides have been made in understanding how the LC binds to the SNARE proteins via X-ray crystallography. Subsequent homology modeling and structure based drug design have led to the discovery of multiple small molecule BoNT/A inhibitors in the 0.05 ~10 μ range, but to date none have shown significant post-symptomatic efficacy in an animal model of botulinum intoxication. With the lack of reported pharmacokinetic data, we have analyzed the BoNT/A inhibitor lead chemical matter from a physicochemical property point of view and have attempted to understand if bioavailability of drug at the neuromuscular junction is the root cause of this apparent in vitro/in vivo disconnect in the field.

Bacillus anthracis, a rod shaped, spore forming, gram positive bacteria, is the etiological agent of anthrax. B. anthracis virulence is partly attributable to two secreted bipartite protein toxins, which act inside host cells to disrupt signaling pathways important for host defense against infection. These toxins may also directly contribute to mortality in late stage infection. The zinc-dependent metalloproteinase anthrax lethal factor (LF) is a critical component of one of these protein toxins and a prime target for inhibitor development to produce anthrax therapeutics. Here, we describe recent efforts to identify specific and potent LF inhibitors. Derivatization of peptide substrate analogs bearing zinc-binding groups has produced potent and specific LF inhibitors, and X-ray crystallography of LFinhibitor complexes has provided insight into features required for high affinity binding. Novel inhibitor scaffolds have been identified through several approaches, including fragment-based drug discovery, virtual screening, and highthroughput screening of diverse compound libraries. Lastly, efforts to discover LF inhibitors have led to the development of new screening strategies, such as the use of full-length proteins as substrates, that may prove useful for other proteases as well. Overall, these efforts have led to a collection of chemically and mechanistically diverse molecules capable of inhibiting LF activity in vitro and in cells, as well as in animal models of anthrax infection.

Among the crowd of bacteria provoking disease of the oral cavity during the weakened of immune system, Streptococcus mutans and Porphyromonas gingivalis are the main microorganisms implicated in caries formation and periodontitis, respectively. The life cycle of the pathogens, such as protozoa, fungi and bacteria, is influenced by a superfamily of enzymes, called carbonic anhydrases (CAs, EC 4.2.1.1). These metalloenzymes, being crucial for the survival of the pathogen, have been considered as novel anti-infective targets. In fact, bicarbonate and protons, produced by the CA catalyzed carbon dioxide as substrate, are two fundamental ions implicated in the pH regulation, biosynthetic reactions, and adaptation of the pathogen to the host or in the possibility of the pathogen to avoid the host immune system. Bacteria genome encodes for the α-, β- and γ-CAs. Recently, our groups using the recombinant DNA technology prepared and characterized the CAs belonging to the β- and γ-classes encoded by the genome of the two oral cavity pathogens S. mutans and P. gingivalis. An extensive inhibition study was carried out using typical anion/sulfonamide inhibitors of these classes of CAs. We discovered numerous inhibitors, which had in vitro an effective inhibitory activity against the bacterial CAs considered, here, as alternative anti-infective targets..

Bacterial infections constitute an always growing health problem worldwide. The resistance to antibiotics of an increasing number of bacterial pathogens necessitates a permanent search for new molecules with different mechanisms of action. Histidine biosynthesis is an ancient pathway found in bacteria, archaebacteria, fungi and plants but absent in mammals. This feature makes it very interesting for the study of new strategies aimed to develop novel classes of antibacterial agents. In particular, one of the enzymes involved in the histidine biosynthesis, i.e. L-histidinol dehydrogenase (HDH), has been demonstrated to be essential for the survival of bacteria associated to several infections, such as brucellosis and tubercolosis. HDH is a Zn²⁺ enzyme which catalyzes the last two steps in the biosynthesis of Lhistidine: sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine. This review will be focused on the biochemical and structural studies performed on HDH so far with the purpose to provide a structural background for the rational drug design of potent HDH inhibitors.

The bacterial enzyme UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC), catalyzing the first committed step of lipid A biosynthesis, represents a promising target in the development of novel antibiotics against Gram-negative bacteria. Structure, catalytic reaction mechanism and regulation of the Zn²⁺-dependent metalloamidase have been intensively investigated. The enzyme is required for growth and viability of Gram-negative bacteria, displays no sequence homology with any mammalian protein, but is highly conserved in Gram-negative bacteria, thus permitting the development of Gram-negative selective antibacterial agents with limited off-target effects. Several smallmolecule LpxC inhibitors have been developed, like the substrate analog TU-514 (12a), the aryloxazoline L-161,240 (13w), the sulfonamide BB-78485 (23a), the N-aroyl-L-threonine derivative CHIR-090 (24a), the sulfone-containing pyridone LpxC-3 (43e), and the uridine-based inhibitor 1-68A (47a), displaying diverse inhibitory and antibacterial activities. Most of these compounds share a Zn²⁺-binding hydroxamate moiety attached to a structural element addressing the hydrophobic tunnel or the UDP binding site. The butadiynyl derivative ACHN-975 (28) is the first LpxC inhibitor entering clinical trials.